Mercurial > repos > recetox > recetox_aplcms_unsupervised

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author recetox
date Fri, 10 Jun 2022 10:14:43 +0000
parents 4e6281945270
children
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d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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1 <tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy3">
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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2 <description>generate a feature table from LC/MS spectra</description>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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3 <macros>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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4 <import>macros.xml</import>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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5 </macros>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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6 <expand macro="creator"/>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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7
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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8 <expand macro="requirements"/>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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9 <command detect_errors="aggressive"><![CDATA[
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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10 sh ${symlink_inputs} &&
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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11 Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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12 ]]></command>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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13 <configfiles>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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14 <configfile name="symlink_inputs">
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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15 #for $infile in $files
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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16 ln -s '${infile}' '${infile.element_identifier}'
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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17 #end for
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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18 </configfile>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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19 <configfile name="run_script"><![CDATA[
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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20 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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21
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22 unsupervised_main(
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23 sample_files = c('$filenames_str'),
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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24 aligned_file = '${aligned_feature_sample_table}',
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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25 recovered_file = '${recovered_feature_sample_table}',
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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26 out_format = '$output_format.out_format',
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27 min_exp = $noise_filtering.min_exp,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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28 min_pres = $noise_filtering.min_pres,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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29 min_run = $noise_filtering.min_run,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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30 mz_tol = $noise_filtering.mz_tol,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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31 baseline_correct = $noise_filtering.baseline_correct,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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32 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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33 intensity_weighted = $noise_filtering.intensity_weighted,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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34 shape_model = '$feature_detection.shape_model',
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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35 BIC_factor = $feature_detection.BIC_factor,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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36 peak_estim_method = '$feature_detection.peak_estim_method',
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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37 min_bandwidth = $feature_detection.min_bandwidth,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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38 max_bandwidth = $feature_detection.max_bandwidth,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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39 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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40 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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41 component_eliminate = $feature_detection.component_eliminate,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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42 moment_power = $feature_detection.moment_power,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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43 align_chr_tol = $peak_alignment.align_chr_tol,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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44 align_mz_tol = $peak_alignment.align_mz_tol,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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45 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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46 recover_mz_range = $weak_signal_recovery.recover_mz_range,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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47 recover_chr_range = $weak_signal_recovery.recover_chr_range,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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48 use_observed_range = $weak_signal_recovery.use_observed_range,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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49 recover_min_count = $weak_signal_recovery.recover_min_count,
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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50 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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51 )
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52 ]]></configfile>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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53 </configfiles>
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54
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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55 <expand macro="inputs">
1
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56 <expand macro="noise_filtering">
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57 <param name="min_exp" type="integer" min="1" value="2"
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58 label="min_exp"
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59 help="If a feature is to be included in the final feature table, it must be present in at least this number of samples." />
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60 </expand>
0
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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61 <expand macro="feature_detection"/>
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62 <expand macro="peak_alignment"/>
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63 <expand macro="weak_signal_recovery"/>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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64 <expand macro="output_format"/>
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65 </expand>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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66
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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67 <outputs>
1
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68 <expand macro="unsupervised_outputs">
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69 <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}">
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70 <discover_datasets pattern="__designation__" directory="extracted" format="parquet" />
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71 </collection >
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72 <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}">
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73 <discover_datasets pattern="__designation__" directory="corrected" format="parquet" />
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74 </collection >
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75 </expand>
0
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76 </outputs>
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77
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78 <tests>
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79 <test>
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80 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
2
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81 <output name="recovered_feature_sample_table" file="unsupervised_output/unsupervised_recovered_feature_sample_table.parquet"
0
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82 ftype="parquet"/>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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83 </test>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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84 <test>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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85 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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86 <section name="output_format">
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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87 <param name="out_format" value="recetox"/>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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88 </section>
2
10093dea9b3f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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89 <output name="recovered_feature_sample_table" file="unsupervised_output/unsupervised.recetox.parquet" ftype="parquet"/>
0
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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90 </test>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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91 </tests>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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92
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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93 <help>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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94 <![CDATA[
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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95 @HELP_unsupervised@
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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96 ]]>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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97 </help>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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98
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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99 <expand macro="citations"/>
d740352d272a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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100 </tool>